Alternative pre-mRNA splicing is a common mechanism for regulating gene expression in metazoans. Indeed, RNA processing is a conduit through which genomic information is transferred to proteomic information. In fact, it is now recognized that 30-40% of the known human and mouse disease gene mutations affect the splicing process. Thus, understanding how introns are recognized and how patterns of alternative splicing are set up may allow therapeutic intervention. Cis-acting sequence elements in the pre- mRNA, known as silencers and enhancers, are known to modulate splice site use. MicroRNAs have been shown to control gene expression at the levels of translation and RNA stability and some microRNAs (and piRNAs or rasiRNAs) act in the nucleus as ribonucleoprotein (RNP) complexes with arognaute/piwi family proteins to alter chromatin structure/organization and control the activity/expression of mobile genetic elements. The overall objective of the research proposed in this grant is to ask if microRNAs can control alternative pre-mRNA splicing patterns in Drosophila using gene expression and splice junction microarrays. Our efforts will be focused on the use of alternative splice junction microarrays along with microRNA blocking or over-expression methods to ask how global splicing patterns change when the function of a single microRNA is perturbed. In order to accomplish our overall objectives, we will: 1. Analyze the genome-wide effects on alternative pre-mRNA splicing patterns using Drosophila splice junction microarrays after blocking microRNA function, blocking microRNA maturation or by using microRNA over-expression in cell culture. 2. Analyze the genome-wide effects on alternative pre-mRNA splicing patterns using Drosophila splice junction microarrays after blocking microRNA function or maturation in whole animals using dicer-1, dicer-2 and ago-2 mutants. PUBLIC HEALTH RELEVANCE Alternative pre-mRNA splicing is a common mechanism for regulating gene expression in metazoans. MicroRNAs have been shown to control gene expression at the levels of translation and RNA stability and some microRNAs (and piRNAs or rasiRNAs) act in the nucleus as ribonucleoprotein (RNP) complexes with arognaute/piwi family proteins to alter chromatin structure/organization and control the activity/expression of mobile genetic elements. The overall objective of the research proposed in this grant is to ask if microRNAs can control alternative pre-mRNA splicing patterns in Drosophila using gene expression and splice junction microarrays.